Compacting a synthetic yeast chromosome arm.
Compacting a synthetic yeast chromosome arm.
复制标题
压缩合成酵母染色体臂
DOI：
10.1186/s13059-020-02232-8
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发表时间：
2021-01-04
期刊：
影响因子：
12.3
通讯作者：
Dai J
中科院分区：
文献类型：
--
作者：
Luo Z;Yu K;Xie S;Monti M;Schindler D;Fang Y;Zhao S;Liang Z;Jiang S;Luan M;Xiao C;Cai Y;Dai J
背景冗余是基因组的一个共同特征，可能是为了确保在不同和不断变化的条件下旺盛的生长。基因组压缩，去除了在特定条件下不必要的序列，为理解生命的核心原理提供了一种新的方法。通过loxP介导的进化系统进行的合成染色体重排和修饰是植入合成酵母基因组(Sc2.0)中的一个独特特征，被认为是基因组最小化的有效工具。随着SC2.0项目的完成，我们开始探索基于置乱系统在基因组压缩中的应用。结果我们提出了一种称为基于置乱的基因组压缩(SGC)的方法，并证明了可以有效地减少合成染色体臂(SynXIIL)。预先引入的上体必需基因阵列显著增强了SGC的紧凑能力，不仅通过删除位于包含loxSquim单位的必需基因中的非必需基因，而且通过允许在单个SGC过程中移除更多的染色体序列。通过迭代SGC实现了进一步的紧凑，揭示了在30 °C的富含介质中，SynxiIL中的65个非必需基因中至少有39个可以被集体移除，而不会影响细胞的存活。约40%的合成序列(编码28个基因)在30 °C的富含介质中对细胞的生长是必不可少的，并鉴定了几个在特定条件下需要功能的基因。结论我们利用eArray建立了迭代的SGC，作为一种通用而有效的工具来压缩合成的酵母基因组。
BackgroundRedundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life. The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system is a unique feature implanted in the synthetic yeast genome (Sc2.0), which is proposed as an effective tool for genome minimization. As the Sc2.0 project is nearing its completion, we have begun to explore the application of the SCRaMbLE system in genome compaction.ResultsWe develop a method termed SCRaMbLE-based genome compaction (SGC) and demonstrate that a synthetic chromosome arm (synXIIL) can be efficiently reduced. The pre-introduced episomal essential gene array significantly enhances the compacting ability of SGC, not only by enabling the deletion of nonessential genes located in essential gene containing loxPsym units but also by allowing more chromosomal sequences to be removed in a single SGC process. Further compaction is achieved through iterative SGC, revealing that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability at 30 °C in rich medium. Approximately 40% of the synthetic sequence, encoding 28 genes, is found to be dispensable for cell growth at 30 °C in rich medium and several genes whose functions are needed under specified conditions are identified.ConclusionsWe develop iterative SGC with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome.
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DOI：
10.1126/science.1135862
发表时间：
2007-02-02
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Driscoll R;Hudson A;Jackson SP
通讯作者：
Jackson SP
影响因子：
7.7
作者：
Breuer, Marian;Earnest, Tyler M.;Luthey-Schulten, Zaida
通讯作者：
Luthey-Schulten, Zaida
影响因子：
64.8
作者：
Dymond, Jessica S.;Richardson, Sarah M.;Coombes, Candice E.;Babatz, Timothy;Muller, Heloise;Annaluru, Narayana;Blake, William J.;Schwerzmann, Joy W.;Dai, Junbiao;Lindstrom, Derek L.;Boeke, Annabel C.;Gottschling, Daniel E.;Chandrasegaran, Srinivasan;Bader, Joel S.;Boeke, Jef D.
通讯作者：
Boeke, Jef D.
影响因子：
56.9
作者：
Han, Junhong;Zhou, Hui;Zhang, Zhiguo
通讯作者：
Zhang, Zhiguo
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng